Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1051 to 1100 of 7460 in total 
Value Type	Ranked
Interaction Map	High confidence

Rank	description	Network Comparison Type	Filtered	red	green	network_comparison	
263	peptide chain release factor 1, mitochondrial precursor (mrf-1). [source:swissprot;acc:o75570]	Subtracted	0	8786.74	7870.3	916.44	
263	protein 1-4 (atp binding protein associated with cell differentiation). [source:swissprot;acc:o14530]	Subtracted	1	242.14	265.696	23.556	
264	60s ribosomal protein l10a (csa-19). [source:swissprot;acc:p53025]	Subtracted	1	243.24	266.796	23.556	
264	arsenical pump-driving atpase (ec 3.6.3.16) (arsenite-translocating atpase) (arsenical resistance atpase) (arsenite-transporting atpase) (arsa) (asna-i). [source:swissprot;acc:o43681]	Divided	0	10037.1	10935.1	1.08947	
264	mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [source:refseq;acc:nm_014026]	Divided	1	219.421	196.978	1.11394	
264	sh2-b homolog; likely ortholog of mouse sh2 domain-containing putative adapter sh2-b; sh2-b gamma signaling protein; sh2-b alpha signaling protein. [source:refseq;acc:nm_015503]	Subtracted	0	12783	13698	915	
265	60s ribosomal protein l9. [source:swissprot;acc:p32969]	Subtracted	1	240.243	263.798	23.555	
265	arsenical pump-driving atpase (ec 3.6.3.16) (arsenite-translocating atpase) (arsenical resistance atpase) (arsenite-transporting atpase) (arsa) (asna-i). [source:swissprot;acc:o43681]	Subtracted	0	10037.1	10935.1	898	
265	glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [source:swissprot;acc:o15488]	Divided	0	13653.8	14874	1.08937	
265	splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [source:swissprot;acc:o75533]	Divided	1	225.217	202.459	1.11241	
266	cysteine endopeptidase aut-like isoform b. [source:refseq;acc:nm_178326]	Subtracted	0	5813.32	6706.32	893	
266	ribosomal protein l10-like protein. [source:refseq;acc:nm_080746]	Subtracted	1	243.12	266.662	23.542	
266	transcription factor btf3 homolog 3. [source:swissprot;acc:q13892]	Divided	0	13483.3	14685.4	1.08915	
266	transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [source:refseq;acc:nm_015477]	Divided	1	241.07	267.88	1.11121	
267	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [source:swissprot;acc:p27635]	Subtracted	1	243.12	266.661	23.541	
267	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [source:swissprot;acc:q10570]	Subtracted	0	10783	11674.1	891.1	
267	density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [source:swissprot;acc:o43583]	Divided	1	241.07	267.88	1.11121	
267	transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [source:swissprot;acc:o00268]	Divided	0	8054.34	8772.02	1.0891	
268	adenylyl cyclase-associated protein 2 (cap 2). [source:swissprot;acc:p40123]	Subtracted	0	10438.3	9549.77	888.53	
268	eukaryotic translation initiation factor 5 (eif-5). [source:swissprot;acc:p55010]	Divided	1	271.016	244.167	1.10996	
268	maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [source:swissprot;acc:q14168]	Divided	0	14257.4	13134.5	1.08549	
268	protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [source:swissprot;acc:o60678]	Subtracted	1	241.625	265.136	23.511	
269	40s ribosomal protein s2 (s4) (llrep3 protein). [source:swissprot;acc:p15880]	Subtracted	1	241.625	265.136	23.511	
269	cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [source:swissprot;acc:p49585]	Divided	1	241.373	267.352	1.10763	
269	ischemia/reperfusion inducible protein. [source:refseq;acc:nm_024640]	Divided	0	12463.5	11482.6	1.08542	
269	mto1 protein homolog (cgi-02). [source:swissprot;acc:q9y2z2]	Subtracted	0	8907.41	9795.36	887.95	
270	40s ribosomal protein s3. [source:swissprot;acc:p23396]	Subtracted	1	241.612	265.119	23.507	
270	associated molecule with the sh3 domain of stam (amsh) like protein. [source:refseq;acc:nm_020799]	Subtracted	0	11644	10763.4	880.6	
270	ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [source:swissprot;acc:q99447]	Divided	0	10735.1	9891.37	1.0853	
270	fad synthetase. [source:refseq;acc:nm_025207]	Divided	1	241.373	267.352	1.10763	
271	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [source:swissprot;acc:o95340]	Divided	1	241.373	267.352	1.10763	
271	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [source:refseq;acc:nm_052936]	Subtracted	0	5781.93	6660.63	878.7	
271	myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [source:swissprot;acc:p12829]	Divided	0	10735.1	9891.37	1.0853	
271	protein transport protein sec61 gamma subunit. [source:swissprot;acc:p38384]	Subtracted	1	243.072	266.559	23.487	
272	fos-related antigen 2. [source:swissprot;acc:p15408]	Subtracted	0	7091.75	6217.28	874.47	
272	ligatin (hepatocellular carcinoma-associated antigen 56). [source:swissprot;acc:p41214]	Divided	1	241.373	267.352	1.10763	
272	mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [source:refseq;acc:nm_022061]	Subtracted	1	242.83	266.248	23.418	
272	sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [source:swissprot;acc:q12772]	Divided	0	7163.55	7759.61	1.08321	
273	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [source:swissprot;acc:o43252]	Divided	1	241.373	267.352	1.10763	
273	disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [source:swissprot;acc:q9p1a6]	Subtracted	0	10432.4	11298.4	866	
273	dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [source:swissprot;acc:p30876]	Subtracted	1	243.208	266.617	23.409	
273	wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [source:swissprot;acc:q9upy6]	Divided	0	12748.1	11770.9	1.08302	
274	40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [source:swissprot;acc:p08865]	Subtracted	0	11977.8	12842.5	864.7	
274	60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [source:swissprot;acc:q9p0j6]	Subtracted	1	242.744	266.07	23.326	
274	disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [source:swissprot;acc:q9p1a6]	Divided	0	10432.4	11298.4	1.08301	
274	nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [source:swissprot;acc:p16435]	Divided	1	241.373	267.352	1.10763	
275	40s ribosomal protein s5. [source:swissprot;acc:p46782]	Subtracted	1	242.473	265.756	23.283	
275	cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [source:swissprot;acc:q9y5k3]	Divided	1	241.373	267.352	1.10763	
275	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [source:swissprot;acc:q10570]	Divided	0	10783	11674.1	1.08264	
275	signal-induced proliferation-associated 1-like 1. [source:refseq;acc:nm_015556]	Subtracted	0	15977.3	15115.5	861.8	

Legend:
- Rank is the rank after comparing the two networks
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.
- http://analysis.yellowcouch.org/